PyCogent

News and Announcements regarding the Python Bioinformatics Toolkit, PyCogent

Archive for the ‘Uncategorized’ Category

PyCogent 1.9 released!!

It’s been a long time coming but it’s finally PyCogent 1.9 release time. I thank all contributors to the library. The developers, documenters and bug reporters. Your efforts are greatly appreciated!

This is a landmark release for a number of reasons. First, it’s been a very long time since the release of 1.5.3. Second, Python 3 is firmly established and the main PyCogent dependencies are now available for it. Third, there have been major changes in the Python and bioinformatics landscape. One of these with direct relevance to PyCogent has been development of scikit-bio. This exciting new project is substantively derived from PyCogent. This and other developments mean we have an excellent opportunity to refocus PyCogent. While more detailed announcements will be made later, I can say that it will become more focussed on statistical comparative molecular evolutionary analyses. It will be ported to Python 3, and there will be at least one other derivative project for the Ensembl querying code.

So stay tuned, exciting developments ahead!

 

Written by gavinhuttley

June 14, 2016 at 10:28 pm

Posted in Uncategorized

PyCogent 1.5.3 released

This is a quick maintenance release to fix an error in the documentation build and a bug in an application controller.

Written by gavinhuttley

September 15, 2012 at 1:15 am

Posted in Uncategorized

PyCogent 1.5.2 released

Many thanks to all the contributors, but a special thanks to Jai Rideout for driving the release through to completion! Check the ChangeLog for details. For users of the Ensembl code, note that while we now support Ensembl release 68 (the latest version at time of writing) Ensembl’s habit of changing their API means this compatibility is quickly broken. In which case, you can obtain the most up-to-date version of the Ensembl code in the svn repository (see instructions here).

Written by gavinhuttley

September 10, 2012 at 5:33 pm

Posted in Uncategorized

PyCogent 1.5.1 released

Many thanks to all the contributors! Despite the minor point release, this version has many new additions. Check the ChangeLog for a summary. Of particular note is we have removed code authored by Ziheng Yang (without loss of functionality) as it is not available under an open source license.

Written by gavinhuttley

June 13, 2011 at 11:22 pm

Posted in Uncategorized

PyCogent 1.5 released

Many thanks to all the contributors for the new features, bug-fixes and performance enhancements. Major additions to the documentation too! As usual, check the ChangeLog for a summary what has gone into this point release. Of particular note are: the inclusion of some parsers for handling next-generatiuon sequencing data; progress display code employed by the cogent.evolve module; and some enhancements to the Ensembl querying code.

Written by gavinhuttley

November 17, 2010 at 11:08 pm

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PyCogent 1.4.1 released

The PyCogent development team is proud to announce the release of PyCogent 1.4.1. This is a minor point release, but includes some exciting new features. Some of the notable additions are the new uclust application controller, which currently supports uclust v1.1.579, and major additions to the Cookbook documentation, courtesy of Tom Elliot. This release supports QIIME 1.0.0 and PyNAST 1.1, whose development teams partially overlap with the PyCogent development team, and which make extensive use of PyCogent.

For more details on the release you should check out the ChangeLog.

Written by Greg Caporaso

April 10, 2010 at 11:22 am

Posted in Uncategorized

PyCogent 1.4 released

The release contains many new features, important changes to the project dependencies and bug-fixes. See the ChangeLog on the PyCogent documentation page for details.

Congratulations and thanks to all the PyCogent Team members for their stellar contributions!

Written by gavinhuttley

December 16, 2009 at 3:06 pm

Posted in Uncategorized